mirror of
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test r language directly
This commit is contained in:
Anthony Sottile
@@ -1,25 +0,0 @@
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# real world
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- id: hello-world
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name: Say hi
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entry: Rscript hello-world.R
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args: [blibla]
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language: r
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types: [r]
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- id: hello-world-inline
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name: Say hi
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entry: |
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Rscript -e
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'stopifnot(
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packageVersion("rprojroot") == "1.0",
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packageVersion("gli.clu") == "0.0.0.9000"
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)
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cat(commandArgs(trailingOnly = TRUE), "from R!\n", sep = ", ")
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'
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args: ['Hi-there']
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language: r
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types: [r]
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- id: additional-deps
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name: Check additional deps
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entry: Rscript additional-deps.R
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language: r
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types: [r]
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@@ -1,19 +0,0 @@
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Package: gli.clu
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Title: What the Package Does (One Line, Title Case)
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Type: Package
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Version: 0.0.0.9000
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Authors@R:
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person(given = "First",
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family = "Last",
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role = c("aut", "cre"),
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email = "first.last@example.com",
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comment = c(ORCID = "YOUR-ORCID-ID"))
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Description: What the package does (one paragraph).
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License: `use_mit_license()`, `use_gpl3_license()` or friends to
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pick a license
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Encoding: UTF-8
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LazyData: true
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.1.1
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Imports:
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rprojroot
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@@ -1,2 +0,0 @@
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suppressPackageStartupMessages(library("cachem"))
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cat("OK\n")
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@@ -1,5 +0,0 @@
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stopifnot(
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packageVersion('rprojroot') == '1.0',
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packageVersion('gli.clu') == '0.0.0.9000'
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)
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cat("Hello, World, from R!\n")
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@@ -1,27 +0,0 @@
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{
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"R": {
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"Version": "4.0.3",
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"Repositories": [
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{
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"Name": "CRAN",
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"URL": "https://cloud.r-project.org"
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}
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]
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},
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"Packages": {
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"renv": {
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"Package": "renv",
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"Version": "0.12.5",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
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},
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"rprojroot": {
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"Package": "rprojroot",
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"Version": "1.0",
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"Source": "Repository",
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"Repository": "CRAN",
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"Hash": "86704667fe0860e4fec35afdfec137f3"
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}
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}
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}
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@@ -1,7 +0,0 @@
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Copyright 2021 RStudio, PBC
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Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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@@ -1,440 +0,0 @@
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local({
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# the requested version of renv
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version <- "0.12.5"
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# the project directory
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project <- getwd()
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# avoid recursion
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if (!is.na(Sys.getenv("RENV_R_INITIALIZING", unset = NA)))
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return(invisible(TRUE))
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# signal that we're loading renv during R startup
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Sys.setenv("RENV_R_INITIALIZING" = "true")
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on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)
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# signal that we've consented to use renv
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options(renv.consent = TRUE)
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# load the 'utils' package eagerly -- this ensures that renv shims, which
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# mask 'utils' packages, will come first on the search path
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library(utils, lib.loc = .Library)
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# check to see if renv has already been loaded
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if ("renv" %in% loadedNamespaces()) {
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# if renv has already been loaded, and it's the requested version of renv,
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# nothing to do
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spec <- .getNamespaceInfo(.getNamespace("renv"), "spec")
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if (identical(spec[["version"]], version))
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return(invisible(TRUE))
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# otherwise, unload and attempt to load the correct version of renv
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unloadNamespace("renv")
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}
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# load bootstrap tools
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bootstrap <- function(version, library) {
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# attempt to download renv
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tarball <- tryCatch(renv_bootstrap_download(version), error = identity)
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if (inherits(tarball, "error"))
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stop("failed to download renv ", version)
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# now attempt to install
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status <- tryCatch(renv_bootstrap_install(version, tarball, library), error = identity)
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if (inherits(status, "error"))
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stop("failed to install renv ", version)
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}
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renv_bootstrap_tests_running <- function() {
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getOption("renv.tests.running", default = FALSE)
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}
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renv_bootstrap_repos <- function() {
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# check for repos override
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repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
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if (!is.na(repos))
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return(repos)
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# if we're testing, re-use the test repositories
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if (renv_bootstrap_tests_running())
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return(getOption("renv.tests.repos"))
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# retrieve current repos
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repos <- getOption("repos")
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# ensure @CRAN@ entries are resolved
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repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
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# add in renv.bootstrap.repos if set
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default <- c(CRAN = "https://cloud.r-project.org")
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extra <- getOption("renv.bootstrap.repos", default = default)
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repos <- c(repos, extra)
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# remove duplicates that might've snuck in
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dupes <- duplicated(repos) | duplicated(names(repos))
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repos[!dupes]
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}
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renv_bootstrap_download <- function(version) {
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# if the renv version number has 4 components, assume it must
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# be retrieved via github
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nv <- numeric_version(version)
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components <- unclass(nv)[[1]]
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methods <- if (length(components) == 4L) {
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list(
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renv_bootstrap_download_github
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)
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} else {
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list(
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renv_bootstrap_download_cran_latest,
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renv_bootstrap_download_cran_archive
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)
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}
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for (method in methods) {
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path <- tryCatch(method(version), error = identity)
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if (is.character(path) && file.exists(path))
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return(path)
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}
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stop("failed to download renv ", version)
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}
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renv_bootstrap_download_impl <- function(url, destfile) {
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mode <- "wb"
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# https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17715
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fixup <-
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Sys.info()[["sysname"]] == "Windows" &&
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substring(url, 1L, 5L) == "file:"
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if (fixup)
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mode <- "w+b"
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utils::download.file(
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url = url,
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destfile = destfile,
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mode = mode,
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quiet = TRUE
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)
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}
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renv_bootstrap_download_cran_latest <- function(version) {
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repos <- renv_bootstrap_download_cran_latest_find(version)
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message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
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info <- tryCatch(
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utils::download.packages(
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pkgs = "renv",
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repos = repos,
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destdir = tempdir(),
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quiet = TRUE
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),
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condition = identity
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)
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if (inherits(info, "condition")) {
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message("FAILED")
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return(FALSE)
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}
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message("OK")
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info[1, 2]
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}
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renv_bootstrap_download_cran_latest_find <- function(version) {
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all <- renv_bootstrap_repos()
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for (repos in all) {
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db <- tryCatch(
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as.data.frame(
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x = utils::available.packages(repos = repos),
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stringsAsFactors = FALSE
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),
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error = identity
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)
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if (inherits(db, "error"))
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next
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entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
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if (nrow(entry) == 0)
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next
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return(repos)
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}
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fmt <- "renv %s is not available from your declared package repositories"
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stop(sprintf(fmt, version))
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}
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renv_bootstrap_download_cran_archive <- function(version) {
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name <- sprintf("renv_%s.tar.gz", version)
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repos <- renv_bootstrap_repos()
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urls <- file.path(repos, "src/contrib/Archive/renv", name)
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destfile <- file.path(tempdir(), name)
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message("* Downloading renv ", version, " from CRAN archive ... ", appendLF = FALSE)
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for (url in urls) {
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status <- tryCatch(
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renv_bootstrap_download_impl(url, destfile),
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condition = identity
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)
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if (identical(status, 0L)) {
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message("OK")
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return(destfile)
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}
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}
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message("FAILED")
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return(FALSE)
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}
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renv_bootstrap_download_github <- function(version) {
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enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
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if (!identical(enabled, "TRUE"))
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return(FALSE)
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# prepare download options
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pat <- Sys.getenv("GITHUB_PAT")
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if (nzchar(Sys.which("curl")) && nzchar(pat)) {
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fmt <- "--location --fail --header \"Authorization: token %s\""
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extra <- sprintf(fmt, pat)
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saved <- options("download.file.method", "download.file.extra")
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options(download.file.method = "curl", download.file.extra = extra)
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on.exit(do.call(base::options, saved), add = TRUE)
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} else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
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fmt <- "--header=\"Authorization: token %s\""
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extra <- sprintf(fmt, pat)
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saved <- options("download.file.method", "download.file.extra")
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options(download.file.method = "wget", download.file.extra = extra)
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on.exit(do.call(base::options, saved), add = TRUE)
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}
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message("* Downloading renv ", version, " from GitHub ... ", appendLF = FALSE)
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url <- file.path("https://api.github.com/repos/rstudio/renv/tarball", version)
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name <- sprintf("renv_%s.tar.gz", version)
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destfile <- file.path(tempdir(), name)
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status <- tryCatch(
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renv_bootstrap_download_impl(url, destfile),
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condition = identity
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)
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if (!identical(status, 0L)) {
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message("FAILED")
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return(FALSE)
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}
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message("OK")
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return(destfile)
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}
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renv_bootstrap_install <- function(version, tarball, library) {
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# attempt to install it into project library
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message("* Installing renv ", version, " ... ", appendLF = FALSE)
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dir.create(library, showWarnings = FALSE, recursive = TRUE)
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# invoke using system2 so we can capture and report output
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bin <- R.home("bin")
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exe <- if (Sys.info()[["sysname"]] == "Windows") "R.exe" else "R"
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r <- file.path(bin, exe)
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args <- c("--vanilla", "CMD", "INSTALL", "-l", shQuote(library), shQuote(tarball))
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output <- system2(r, args, stdout = TRUE, stderr = TRUE)
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message("Done!")
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# check for successful install
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status <- attr(output, "status")
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if (is.numeric(status) && !identical(status, 0L)) {
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header <- "Error installing renv:"
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lines <- paste(rep.int("=", nchar(header)), collapse = "")
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text <- c(header, lines, output)
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writeLines(text, con = stderr())
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}
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status
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}
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renv_bootstrap_prefix <- function() {
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# construct version prefix
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version <- paste(R.version$major, R.version$minor, sep = ".")
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prefix <- paste("R", numeric_version(version)[1, 1:2], sep = "-")
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# include SVN revision for development versions of R
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# (to avoid sharing platform-specific artefacts with released versions of R)
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devel <-
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identical(R.version[["status"]], "Under development (unstable)") ||
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identical(R.version[["nickname"]], "Unsuffered Consequences")
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if (devel)
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prefix <- paste(prefix, R.version[["svn rev"]], sep = "-r")
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# build list of path components
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components <- c(prefix, R.version$platform)
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# include prefix if provided by user
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prefix <- Sys.getenv("RENV_PATHS_PREFIX")
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if (nzchar(prefix))
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components <- c(prefix, components)
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# build prefix
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paste(components, collapse = "/")
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}
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renv_bootstrap_library_root_name <- function(project) {
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# use project name as-is if requested
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asis <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT_ASIS", unset = "FALSE")
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if (asis)
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return(basename(project))
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# otherwise, disambiguate based on project's path
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id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
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paste(basename(project), id, sep = "-")
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}
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renv_bootstrap_library_root <- function(project) {
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path <- Sys.getenv("RENV_PATHS_LIBRARY", unset = NA)
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if (!is.na(path))
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return(path)
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path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
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if (!is.na(path)) {
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name <- renv_bootstrap_library_root_name(project)
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return(file.path(path, name))
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}
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file.path(project, "renv/library")
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||||
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||||
}
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||||
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renv_bootstrap_validate_version <- function(version) {
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loadedversion <- utils::packageDescription("renv", fields = "Version")
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if (version == loadedversion)
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return(TRUE)
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||||
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# assume four-component versions are from GitHub; three-component
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||||
# versions are from CRAN
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components <- strsplit(loadedversion, "[.-]")[[1]]
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remote <- if (length(components) == 4L)
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paste("rstudio/renv", loadedversion, sep = "@")
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||||
else
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||||
paste("renv", loadedversion, sep = "@")
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||||
|
||||
fmt <- paste(
|
||||
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
|
||||
"Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
|
||||
"Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
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sep = "\n"
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)
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||||
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||||
msg <- sprintf(fmt, loadedversion, version, remote)
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||||
warning(msg, call. = FALSE)
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||||
|
||||
FALSE
|
||||
|
||||
}
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||||
|
||||
renv_bootstrap_hash_text <- function(text) {
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||||
|
||||
hashfile <- tempfile("renv-hash-")
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||||
on.exit(unlink(hashfile), add = TRUE)
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||||
|
||||
writeLines(text, con = hashfile)
|
||||
tools::md5sum(hashfile)
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_load <- function(project, libpath, version) {
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||||
|
||||
# try to load renv from the project library
|
||||
if (!requireNamespace("renv", lib.loc = libpath, quietly = TRUE))
|
||||
return(FALSE)
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||||
|
||||
# warn if the version of renv loaded does not match
|
||||
renv_bootstrap_validate_version(version)
|
||||
|
||||
# load the project
|
||||
renv::load(project)
|
||||
|
||||
TRUE
|
||||
|
||||
}
|
||||
|
||||
# construct path to library root
|
||||
root <- renv_bootstrap_library_root(project)
|
||||
|
||||
# construct library prefix for platform
|
||||
prefix <- renv_bootstrap_prefix()
|
||||
|
||||
# construct full libpath
|
||||
libpath <- file.path(root, prefix)
|
||||
|
||||
# attempt to load
|
||||
if (renv_bootstrap_load(project, libpath, version))
|
||||
return(TRUE)
|
||||
|
||||
# load failed; inform user we're about to bootstrap
|
||||
prefix <- paste("# Bootstrapping renv", version)
|
||||
postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
|
||||
header <- paste(prefix, postfix)
|
||||
message(header)
|
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|
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# perform bootstrap
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bootstrap(version, libpath)
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|
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# exit early if we're just testing bootstrap
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if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
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return(TRUE)
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|
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# try again to load
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if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
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message("* Successfully installed and loaded renv ", version, ".")
|
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return(renv::load())
|
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}
|
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|
||||
# failed to download or load renv; warn the user
|
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msg <- c(
|
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"Failed to find an renv installation: the project will not be loaded.",
|
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"Use `renv::activate()` to re-initialize the project."
|
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)
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warning(paste(msg, collapse = "\n"), call. = FALSE)
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|
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})
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@@ -1,13 +1,16 @@
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from __future__ import annotations
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import os.path
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import shutil
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|
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import pytest
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|
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from pre_commit import envcontext
|
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from pre_commit.languages import r
|
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from pre_commit.prefix import Prefix
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from pre_commit.store import _make_local_repo
|
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from pre_commit.util import win_exe
|
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from testing.language_helpers import run_language
|
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|
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|
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def test_r_parsing_file_no_opts_no_args(tmp_path):
|
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@@ -97,3 +100,99 @@ def test_rscript_exec_relative_to_r_home():
|
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def test_path_rscript_exec_no_r_home_set():
|
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with envcontext.envcontext((('R_HOME', envcontext.UNSET),)):
|
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assert r._rscript_exec() == 'Rscript'
|
||||
|
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|
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def test_r_hook(tmp_path):
|
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renv_lock = '''\
|
||||
{
|
||||
"R": {
|
||||
"Version": "4.0.3",
|
||||
"Repositories": [
|
||||
{
|
||||
"Name": "CRAN",
|
||||
"URL": "https://cloud.r-project.org"
|
||||
}
|
||||
]
|
||||
},
|
||||
"Packages": {
|
||||
"renv": {
|
||||
"Package": "renv",
|
||||
"Version": "0.12.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "5c0cdb37f063c58cdab3c7e9fbb8bd2c"
|
||||
},
|
||||
"rprojroot": {
|
||||
"Package": "rprojroot",
|
||||
"Version": "1.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "86704667fe0860e4fec35afdfec137f3"
|
||||
}
|
||||
}
|
||||
}
|
||||
'''
|
||||
description = '''\
|
||||
Package: gli.clu
|
||||
Title: What the Package Does (One Line, Title Case)
|
||||
Type: Package
|
||||
Version: 0.0.0.9000
|
||||
Authors@R:
|
||||
person(given = "First",
|
||||
family = "Last",
|
||||
role = c("aut", "cre"),
|
||||
email = "first.last@example.com",
|
||||
comment = c(ORCID = "YOUR-ORCID-ID"))
|
||||
Description: What the package does (one paragraph).
|
||||
License: `use_mit_license()`, `use_gpl3_license()` or friends to
|
||||
pick a license
|
||||
Encoding: UTF-8
|
||||
LazyData: true
|
||||
Roxygen: list(markdown = TRUE)
|
||||
RoxygenNote: 7.1.1
|
||||
Imports:
|
||||
rprojroot
|
||||
'''
|
||||
hello_world_r = '''\
|
||||
stopifnot(
|
||||
packageVersion('rprojroot') == '1.0',
|
||||
packageVersion('gli.clu') == '0.0.0.9000'
|
||||
)
|
||||
cat("Hello, World, from R!\n")
|
||||
'''
|
||||
|
||||
tmp_path.joinpath('renv.lock').write_text(renv_lock)
|
||||
tmp_path.joinpath('DESCRIPTION').write_text(description)
|
||||
tmp_path.joinpath('hello-world.R').write_text(hello_world_r)
|
||||
renv_dir = tmp_path.joinpath('renv')
|
||||
renv_dir.mkdir()
|
||||
shutil.copy(
|
||||
os.path.join(
|
||||
os.path.dirname(__file__),
|
||||
'../../pre_commit/resources/empty_template_activate.R',
|
||||
),
|
||||
renv_dir.joinpath('activate.R'),
|
||||
)
|
||||
|
||||
expected = (0, b'Hello, World, from R!\n')
|
||||
assert run_language(tmp_path, r, 'Rscript hello-world.R') == expected
|
||||
|
||||
|
||||
def test_r_inline(tmp_path):
|
||||
_make_local_repo(str(tmp_path))
|
||||
|
||||
cmd = '''\
|
||||
Rscript -e '
|
||||
stopifnot(packageVersion("rprojroot") == "1.0")
|
||||
cat(commandArgs(trailingOnly = TRUE), "from R!\n", sep=", ")
|
||||
'
|
||||
'''
|
||||
|
||||
ret = run_language(
|
||||
tmp_path,
|
||||
r,
|
||||
cmd,
|
||||
deps=('rprojroot@1.0',),
|
||||
args=('hi', 'hello'),
|
||||
)
|
||||
assert ret == (0, b'hi, hello, from R!\n')
|
||||
|
||||
@@ -227,54 +227,6 @@ def test_node_hook_with_npm_userconfig_set(tempdir_factory, store, tmpdir):
|
||||
test_run_a_node_hook(tempdir_factory, store)
|
||||
|
||||
|
||||
def test_r_hook(tempdir_factory, store):
|
||||
_test_hook_repo(
|
||||
tempdir_factory, store, 'r_hooks_repo',
|
||||
'hello-world', [os.devnull],
|
||||
b'Hello, World, from R!\n',
|
||||
)
|
||||
|
||||
|
||||
def test_r_inline_hook(tempdir_factory, store):
|
||||
_test_hook_repo(
|
||||
tempdir_factory, store, 'r_hooks_repo',
|
||||
'hello-world-inline', ['some-file'],
|
||||
b'Hi-there, some-file, from R!\n',
|
||||
)
|
||||
|
||||
|
||||
def test_r_with_additional_dependencies_hook(tempdir_factory, store):
|
||||
_test_hook_repo(
|
||||
tempdir_factory, store, 'r_hooks_repo',
|
||||
'additional-deps', [os.devnull],
|
||||
b'OK\n',
|
||||
config_kwargs={
|
||||
'hooks': [{
|
||||
'id': 'additional-deps',
|
||||
'additional_dependencies': ['cachem@1.0.4'],
|
||||
}],
|
||||
},
|
||||
)
|
||||
|
||||
|
||||
def test_r_local_with_additional_dependencies_hook(store):
|
||||
config = {
|
||||
'repo': 'local',
|
||||
'hooks': [{
|
||||
'id': 'local-r',
|
||||
'name': 'local-r',
|
||||
'entry': 'Rscript -e',
|
||||
'language': 'r',
|
||||
'args': ['if (packageVersion("R6") == "2.1.3") cat("OK\n")'],
|
||||
'additional_dependencies': ['R6@2.1.3'],
|
||||
}],
|
||||
}
|
||||
hook = _get_hook(config, store, 'local-r')
|
||||
ret, out = _hook_run(hook, (), color=False)
|
||||
assert ret == 0
|
||||
assert _norm_out(out) == b'OK\n'
|
||||
|
||||
|
||||
def test_run_a_ruby_hook(tempdir_factory, store):
|
||||
_test_hook_repo(
|
||||
tempdir_factory, store, 'ruby_hooks_repo',
|
||||
|
||||
Reference in New Issue
Block a user